Rhizosphere impacts bacterial community structure in the tea (Camellia sinensis (L.) O. Kuntze.) estates of Darjeeling, India.

India contributes 28% of the world's tea production, and the Darjeeling tea of India is a world-famous tea variety known for its unique quality, flavour and aroma. This study analyzed the spatial distribution of bacterial communities in the tea rhizosphere of six different tea estates at different altitudes. The organic carbon, total nitrogen and available phosphate were higher in the rhizosphere soils than the bulk soils, irrespective of the sites. Alpha and beta diversities were significantly (p < 0.05) higher in the bulk soil than in the rhizosphere. Among the identified phyla, the predominant ones were Proteobacteria, Actinobacteria and Acidobacteria. At the genus level, only four out of 23 predominant genera (>1% relative abundance) could be classified, viz., Candidatus Solibacter (5.36 ± 0.36%), Rhodoplanes (4.87 ± 0.3%), Candidatus Koribacter (2.3 ± 0.67%), Prevotella (1.49 ± 0.26%). The rhizosphere effect was prominent from the significant depletion of more ASVs (n = 39) compared to enrichment (n = 11). The functional genes also exhibit a similar trend with the enrichment of N2 fixation genes, disease suppression and Acetoin synthesis. Our study reports that the rhizobiome of tea is highly selective by reducing the alpha and beta diversity while enriching the significant functional genes.

Evaluation of plant growth promotion properties and induction of antioxidative defense mechanism by tea rhizobacteria of Darjeeling, India.

A total of 120 rhizobacteria were isolated from seven different tea estates of Darjeeling, West Bengal, India. Based on a functional screening of in vitro plant growth-promoting (PGP) activities, thirty potential rhizobacterial isolates were selected for in-planta evaluation of PGP activities in rice and maize crops. All the thirty rhizobacterial isolates were identified using partial 16S rRNA gene sequencing. Out of thirty rhizobacteria, sixteen (53.3%) isolates belong to genus Bacillus, five (16.6%) represent genus Staphylococcus, three (10%) represent genus Ochrobactrum, and one (3.3%) isolate each belongs to genera Pseudomonas, Lysinibacillus, Micrococcus, Leifsonia, Exiguobacterium, and Arthrobacter. Treatment of rice and maize seedlings with these thirty rhizobacterial isolates resulted in growth promotion. Besides, rhizobacterial treatment in rice triggered enzymatic [ascorbate peroxidase (APX), catalase (CAT), chitinase, and phenylalanine ammonia-lyase (PAL)], and non-enzymatic [proline and polyphenolics] antioxidative defense reactions indicating their possible role in the reduction of reactive oxygen species (ROS) burden and thereby priming of plants towards stress mitigation. To understand such a possibility, we tested the effect of rhizobacterial consortia on biotic stress tolerance of rice against necrotrophic fungi, Rhizoctonia solani AG1-IA. Our results indicated that the pretreatment with rhizobacterial consortia increased resistance of the rice plants towards the common foliar pathogen like R. solani AG1-IA. This study supports the idea of the application of plant growth-promoting rhizobacterial consortia in sustainable crop practice through the management of biotic stress under field conditions.

Microbial and plant-assisted heavy metal remediation in aquatic ecosystems: a comprehensive review.

Heavy metal (HM) pollution in aquatic ecosystems has an adverse effect on both aquatic life forms as well as terrestrial living beings, including humans. Since HMs are recalcitrant, they accumulate in the environment and are subsequently biomagnified through the food chain. Conventional physical and chemical methods used to remove the HMs from aquatic habitats are usually expensive, slow, non-environment friendly, and mostly inefficient. On the contrary, phytoremediation and microbe-assisted remediation technologies have attracted immense attention in recent years and offer a better solution to the problem. These newly emerged remediation technologies are eco-friendly, efficient and cost-effective. Both phytoremediation and microbe-assisted remediation technologies adopt different mechanisms for HM bioremediation in aquatic ecosystems. Recent advancement of molecular tools has contributed significantly to better understand the mechanisms of metal adsorption, translocation, sequestration, and tolerance in plants and microbes. Albeit immense possibilities to use such bioremediation as a successful environmental clean-up technology, it is yet to be successfully implemented in the field conditions. This review article comprehensively discusses HM accumulation in Indian aquatic environments. Furthermore, it describes the effect of HMs accumulation in the aquatic environment and the role of phytoremediation as well as microbe-assisted remediation in mitigation of the HM toxicity. Finally, the review concludes with a note on the challenges, opportunities and future directions for bioremediation in the aquatic ecosystems.

Diversity of fungi from mangrove sediments of Goa, India, obtained by metagenomic analysis using Illumina sequencing.

The fungal composition, abundance and diversity of the mangrove sediments from the Mandovi and Zuari estuaries, Goa, using paired-end Illumina sequencing, hitherto unexplored by a metagenomic approach, indicated that though the types of fungal phyla were similar between the two sediments, the abundance of the species was significantly different between them (p value < 0.005). Basidiomycota and Ascomycota were the two major phyla which were sub-divided into eighteen classes, families, orders, genera and species and one unassigned group in both the sediments. The top five classes observed were Agaricomycetes, Sordariomycetes, Saccharomycetes, Dothideomycetes and Eurotiomycetes from both the sediments. The diversity analysis based on the observed fungal species richness (Chao 1 for Mandovi were 614 and 714.7 while for Zuari were 665 and 771.2) revealed that Zuari sediment was taxonomically rich, indicating these to be potent candidates for bioremediation and a rich repository for biotechnologically important fungi. This is a first report on diversity of fungi from mangrove sediments of Goa using metagenomic studies.

Taxonomic diversity of bacteria from mangrove sediments of Goa: metagenomic and functional analysis.

The present study compared the taxonomic diversity and evaluated the functional attributes of the bacterial species from Mandovi and Zuari mangrove sediments, Goa, using paired-end amplicon sequencing of 16S rDNA and culture-based analyses, respectively. 16S rDNA sequencing revealed Proteobacteria, Firmicutes, and Actinobacteria as the dominant phyla in both the sediments. However, the abundance of these phyla significantly differed between the samples. Bacteroidetes from Mandovi sediment, and Acidobacteria and Gemmatimonadetes from Zuari sediment were the other exclusive major phyla. Chloroflexi, Cyanobacteria, Nitrospirae, Planctomycetes, Verrucomicrobia, and WS3 were the minor phyla observed in both. However, a significant difference in the distribution of minor phyla and lower bacterial taxa under each phylum was noted between the sediments, indicating that the resident microbial flora completely differed between them. This was further validated by high values from distance matrix analyses between the samples. In addition, the pathogenic Vibrio sp. was recorded exclusively in Mandovi sediment, while higher abundance of ecologically important bacterial classes including Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, and Bacilli was observed in Zuari sediment. Taken together, the data indicated that Zuari sediment was taxonomically richer than Mandovi sediment, while a greater incidence of anthropogenic activities occurred in the latter. This observation was further validated by non-parametric richness estimators which were found to be higher for Zuari sediment. The cultured bacterial isolates, all identified as Firmicutes, were tested for activities related to biofertilization and production of enzymes to be used for bioremediation and chemotherapeutic applications. Higher number of bacterial isolates from Mandovi was found to produce indole-acetic-acid, tannase, xylanase, and glutaminase enzymes, and could solubilize phosphate. In contrast, higher proportion of bacterial isolates from Zuari sediment were capable of producing amylase, cellulase, gelatinase, laccase, lipase, protease, and asparaginase enzymes, emphasizing the fact that the Zuari mangrove sediment is a rich reservoir for economically and biotechnologically important bacterial species.

Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential.

Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration.

Impact of plant development on the rhizobacterial population of Arachis hypogaea: a multifactorial analysis.

Present study investigates the impact of plant development on the structure and composition of root-associated bacterial community of groundnut (Arachis hypogaea) plant, an economically important oilseed legume. Relative abundance of total and active bacteria were studied in bulk soil and rhizosphere samples collected from different growth stages of groundnut plant by sequencing PCR-amplified 16S rRNA gene fragments from soil genomic DNA and reverse-transcribed soil community RNA. Plant growth promoting potential of cultivable rhizobacteria was evaluated using assays for inorganic phosphate solubilization and production of indole acetic acid, siderophores, biofilm, 1-amino-cyclopropane-1-carboxylate deaminase, laccase, and anti-fungal chemicals. Our study demonstrates that groundnut plant rhizosphere harbors a core microbiome populated by Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria. A distinct bacterial assemblage at nodulation stage due to predominance of Flavobacteria and Actinobacteria in DNA and RNA derived libraries respectively was also observed. Majority of cultivable isolates exhibiting plant growth promoting activities belonged to Proteobacteria and Firmicutes. Of them, Pseudomonas indica and Bacillus megaterium were detected in the rhizosphere samples from all the developmental stages of groundnut plant. This polyphasic study establishes the impact of plant development on rhizobacterial population of groundnut and underscores the applicability of soil isolates as a reliable component in sustainable agriculture.

Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea.

Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alpha-proteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes. Most bacterial isolates from the groundnut-rhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system.